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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This example shows how RGroupDecomposition works with stereochemistry matching.\n",
    "If stereochemistry is specified in the core, the RGroup decomposition correctly assigns R1 and R2."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/kellebr5/anaconda/lib/python2.7/site-packages/ipykernel/__main__.py:4: RuntimeWarning: to-Python converter for std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > already registered; second conversion method ignored.\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "IPythonConsole.ipython_useSVG=True\n",
    "from rdkit.Chem import rdRGroupDecomposition"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from rdkit.Chem import PandasTools"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "m = Chem.MolFromSmarts(\"C1CCO[C@@](*)(*)1\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Perhaps we should file a bug that smarts doesn't show stereochem here."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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    "m"
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Make some example stereochemistries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "C1CCO[C@@H](N)1\n",
      "C1CCO[C@H](N)1\n",
      "C1CCO[C@@](N)(O)1\n",
      "C1CCO[C@@](N)(P)1\n",
      "C1CCO[C@@](N)(S)1\n",
      "C1CCO[C@@H](O)1\n",
      "C1CCO[C@H](O)1\n",
      "C1CCO[C@@](O)(N)1\n",
      "C1CCO[C@@](O)(P)1\n",
      "C1CCO[C@@](O)(S)1\n",
      "C1CCO[C@@H](P)1\n",
      "C1CCO[C@H](P)1\n",
      "C1CCO[C@@](P)(N)1\n",
      "C1CCO[C@@](P)(O)1\n",
      "C1CCO[C@@](P)(S)1\n",
      "C1CCO[C@@H](S)1\n",
      "C1CCO[C@H](S)1\n",
      "C1CCO[C@@](S)(N)1\n",
      "C1CCO[C@@](S)(O)1\n",
      "C1CCO[C@@](S)(P)1\n"
     ]
    }
   ],
   "source": [
    "el = \"NOPS\"\n",
    "mols = []\n",
    "for e in el:\n",
    "    smi = \"C1CCO[C@@H](%s)1\"%e\n",
    "    print(smi)\n",
    "    m = Chem.MolFromSmiles(smi)\n",
    "    mols.append(m)\n",
    "    smi = \"C1CCO[C@H](%s)1\"%e\n",
    "    print(smi)\n",
    "    m = Chem.MolFromSmiles(smi)\n",
    "    mols.append(m)\n",
    "    for e2 in el:\n",
    "        if e != e2:\n",
    "            smi = \"C1CCO[C@@](%s)(%s)1\"%(e,e2)\n",
    "            m = Chem.MolFromSmiles(smi)\n",
    "            if m:\n",
    "                print(smi)\n",
    "                mols.append(m)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
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   "outputs": [
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      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from rdkit.Chem import Draw\n",
    "Draw.MolsToGridImage(mols)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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       "<path d=\"M 51.1512,122.857 38.5531,119.024\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path d=\"M 38.5531,119.024 25.9549,115.192\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"51.1512\" y=\"130.803\"><tspan>N</tspan></text>\n",
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       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000\" x=\"117.452\" y=\"169.305\"><tspan>H</tspan></text>\n",
       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000\" x=\"77.4026\" y=\"153.983\"><tspan>H</tspan></text>\n",
       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000\" x=\"174.558\" y=\"118.147\"><tspan>H</tspan></text>\n",
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       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000\" x=\"173.995\" y=\"88.3098\"><tspan>H</tspan></text>\n",
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       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000\" x=\"57.3454\" y=\"43.2718\"><tspan>H</tspan></text>\n",
       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000\" x=\"14.5413\" y=\"92.6532\"><tspan>H</tspan></text>\n",
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       "<path d=\"M 102.687,130.182 81.9692,142.332\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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       "<text style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"48.4724\" y=\"125.489\"><tspan>N</tspan></text>\n",
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     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hmols = [Chem.AddHs(m) for m in mols]\n",
    "Draw.MolsToGridImage(hmols)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "core = Chem.MolFromSmarts(\"C1CCO[C@@](*)(*)1\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Make RGroup decomposition!\n",
    "\n",
    "To use RGroupDecomposition:\n",
    "  \n",
    "  1. construct the class on the core rg = RGroupDecomposition(core)\n",
    "  2. Call rg.Add( mol ) on the molecules.  If this returns -1, the molecule is not\n",
    "     compatible with the core\n",
    "  3. After all molecules are added, call rg.Process() to complete the rgroup\n",
    "     decomposition."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "rgroups = rdRGroupDecomposition.RGroupDecomposition(core)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "for i,m in enumerate(mols):\n",
    "    rgroups.Add(m)\n",
    "    if i == 10:\n",
    "        break"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We need to call process after all molecules are added.  To optimize the RGroups."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rgroups.Process()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The RGroupDecomposition code is quite compatiable with the python pandas integration.\n",
    "Calling rg.GetRGroupsAsColumns() can be sent directly into a pandas table.\n",
    "\n",
    "**n.b.** You need to call PandasTools.ChangeMoleculeRendering(frame) to allow the molecules\n",
    "to be rendered properly."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "groups = rgroups.GetRGroupsAsColumns()\n",
    "frame = pd.DataFrame(groups)\n",
    "PandasTools.ChangeMoleculeRendering(frame)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The first two (0 and 1) are different due to the sterochemistry difference.\n",
    "I still haven't found a way to show the core with stereochem which is annoying."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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       "8   <img src=\"\" alt=\"Mol\"/>  <img src=\"\" alt=\"Mol\"/>                                          <img src=\"\" alt=\"Mol\"/>\n",
       "9   <img src=\"\" alt=\"Mol\"/>                          <img src=\"\" alt=\"Mol\"/>                                          <img src=\"\" alt=\"Mol\"/>\n",
       "10  <img src=\"\" alt=\"Mol\"/>  <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                                          <img src=\"\" alt=\"Mol\"/>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frame"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "Let's try the same with stereochemistry in the core.\n",
    "\n",
    "**Note that the core has symmetry and the analysis nicely supports this during \n",
    "the side chain optimization**\n",
    "\n",
    "**n.b.** stereo information is lost here which is fairly annoying and will be analyzed at a later date."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Core</th>\n",
       "      <th>R1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "      <td><img src=\"\" alt=\"Mol\"/></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>"
      ],
      "text/plain": [
       "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Core                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     R1\n",
       "0   <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "1   <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "2   <img src=\"\" alt=\"Mol\"/>                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "3   <img src=\"\" alt=\"Mol\"/>          <img src=\"\" alt=\"Mol\"/>\n",
       "4   <img src=\"\" alt=\"Mol\"/>                          <img src=\"\" alt=\"Mol\"/>\n",
       "5   <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                                                                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "6   <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                                                                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "7   <img src=\"\" alt=\"Mol\"/>                                                                                                  <img src=\"\" alt=\"Mol\"/>\n",
       "8   <img src=\"\" alt=\"Mol\"/>                                                                              <img src=\"\" alt=\"Mol\"/>\n",
       "9   <img src=\"\" alt=\"Mol\"/>                                                                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "10  <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                              <img src=\"\" alt=\"Mol\"/>\n",
       "11  <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                              <img src=\"\" alt=\"Mol\"/>\n",
       "12  <img src=\"\" alt=\"Mol\"/>  <img src=\"\" alt=\"Mol\"/>\n",
       "13  <img src=\"\" alt=\"Mol\"/>                                              <img src=\"\" alt=\"Mol\"/>\n",
       "14  <img src=\"\" alt=\"Mol\"/>                  <img src=\"\" alt=\"Mol\"/>\n",
       "15  <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                                                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "16  <img src=\"\" alt=\"Mol\"/>                                                                                                                                                                                                                                      <img src=\"\" alt=\"Mol\"/>\n",
       "17  <img src=\"\" alt=\"Mol\"/>                                                          <img src=\"\" alt=\"Mol\"/>\n",
       "18  <img src=\"\" alt=\"Mol\"/>                                                                                                              <img src=\"\" alt=\"Mol\"/>\n",
       "19  <img src=\"\" alt=\"Mol\"/>                                              <img src=\"\" alt=\"Mol\"/>"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "core = Chem.MolFromSmarts(\"C1CCOC1\")\n",
    "rgroups = rdRGroupDecomposition.RGroupDecomposition(core)\n",
    "for m in mols:\n",
    "    rgroups.Add(m)\n",
    "rgroups.Process()\n",
    "frame = pd.DataFrame(rgroups.GetRGroupsAsColumns())\n",
    "PandasTools.ChangeMoleculeRendering(frame)\n",
    "frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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